US border agents have neglected and physically and sexually abused more than 100 migrant children who were in their custody, according to a scathing new report.

The report from the American Civil Liberties Union (ACLU) and the University of Chicago Law School International Human Rights Clinic is based on thousands of pages of records detailing accusations from 116 unaccompanied migrant children in temporary US detention centers.

Some minors accused US Customs and Border Protection (CBP) agents of punching or kicking them and running them over with vehicles. Others said they were tased and verbally abused by officers.

Children also complained of being deprived of edible food and water, held in freezing cells, touched inappropriately by officers and threatened with rape or death.

“Migrant children long have reported varied mistreatment in CBP custody, including sexual, physical, and verbal abuse, and the deprivation of basic needs such as food, water, and emergency medical care,” the ACLU said in a summary of the report.

The report accuses the Department of Homeland Security (DHS) of violating federal law by not reporting the alleged abuses to the FBI.

The accusations stem from 30,000 pages of records relating to abuses between 2009 and 2014.

“These records document a pattern of intimidation, harassment, physical abuse, refusal of medical services, and improper deportation,” the report said. “These failures have allowed a culture of impunity to flourish within CBP.”

The DHS has faced scrutiny for covering up alleged abuses in the past. In 2014, the department investigated allegations from the ACLU of abuse against unaccompanied minors, concluding that it could not “substantiate any of the allegations.”

In the new report, the ACLU said the past investigations by the DHS “indicate systemic failures to meaningfully investigate the allegations."

President Donald Trump signed an executive order in April directing Defense Secretary James Mattis to support the DHS in combating a “drastic surge of illegal activity on the southern border.”

In line with that directive, the Pentagon has recently approved a DHS request for more than 700 National Guard troops to supplement border agents in several southwestern states.